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Q9BY41

- HDAC8_HUMAN

UniProt

Q9BY41 - HDAC8_HUMAN

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Protein

Histone deacetylase 8

Gene

HDAC8

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Also involved in the deacetylation of cohesin complex protein SMC3 regulating release of cohesin complexes from chromatin. May play a role in smooth muscle cell contractility.5 Publications

Catalytic activityi

Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.

Cofactori

a divalent metal cationNote: Binds 1 divalent metal cation per subunit.

Enzyme regulationi

Its activity is inhibited by trichostatin A (TSA), suberoylanilide hydroxamic acid (SAHA), 3-(1-methyl-4-phenylacetyl-1H-2-pyrrolyl)-N-hydroxy-2-propenamide (APHA), 4-dimethylamino-N-(6-hydroxycarbamoyethyl)benzamide-N-hydroxy-7-(4-dimethylaminobenzoyl)aminoheptanamide (MS-344), 5-(4-methyl-benzoylamino)-biphenyl-3,4'-dicarboxylic acid 3-dimethylamide 4'-hydroxyamide (CRA-A) and butyrate.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei101 – 1011Substrate
Active sitei143 – 1431Proton acceptor1 Publication
Binding sitei151 – 1511Substrate; via carbonyl oxygen
Metal bindingi178 – 1781Divalent metal cation1 Publication
Metal bindingi180 – 1801Divalent metal cation1 Publication
Metal bindingi267 – 2671Divalent metal cation1 Publication
Binding sitei306 – 3061Substrate

GO - Molecular functioni

  1. histone deacetylase activity Source: UniProtKB
  2. metal ion binding Source: UniProtKB-KW
  3. NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
  4. NAD-dependent histone deacetylase activity (H3-K18 specific) Source: UniProtKB-EC
  5. NAD-dependent histone deacetylase activity (H3-K9 specific) Source: UniProtKB-EC
  6. NAD-dependent histone deacetylase activity (H4-K16 specific) Source: UniProtKB-EC
  7. transcription factor binding Source: UniProtKB

GO - Biological processi

  1. chromatin assembly or disassembly Source: ProtInc
  2. chromatin modification Source: UniProtKB
  3. mitotic cell cycle Source: Reactome
  4. negative regulation of transcription from RNA polymerase II promoter Source: ProtInc
  5. regulation of cohesin localization to chromatin Source: UniProtKB
  6. sister chromatid cohesion Source: UniProtKB
  7. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Hydrolase, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

BRENDAi3.5.1.98. 2681.
ReactomeiREACT_118780. NOTCH1 Intracellular Domain Regulates Transcription.
REACT_150425. Resolution of Sister Chromatid Cohesion.
REACT_150471. Separation of Sister Chromatids.
REACT_160243. Constitutive Signaling by NOTCH1 PEST Domain Mutants.
REACT_160254. Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants.
REACT_228222. HDACs deacetylate histones.
SABIO-RKQ9BY41.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase 8 (EC:3.5.1.98)
Short name:
HD8
Gene namesi
Name:HDAC8
Synonyms:HDACL1
ORF Names:CDA07
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome X

Organism-specific databases

HGNCiHGNC:13315. HDAC8.

Subcellular locationi

Nucleus. Cytoplasm
Note: Excluded from the nucleoli. Found in the cytoplasm of cells showing smooth muscle differentiation.

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. cytosol Source: Reactome
  3. histone deacetylase complex Source: UniProtKB
  4. nuclear chromosome Source: ProtInc
  5. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

Cornelia de Lange syndrome 5 (CDLS5) [MIM:300882]: A form of Cornelia de Lange syndrome, a clinically heterogeneous developmental disorder associated with malformations affecting multiple systems. It is characterized by facial dysmorphisms, abnormal hands and feet, growth delay, cognitive retardation, hirsutism, gastroesophageal dysfunction and cardiac, ophthalmologic and genitourinary anomalies.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti180 – 1801H → R in CDLS5. 1 Publication
VAR_069140
Natural varianti311 – 3111T → M in CDLS5. 1 Publication
VAR_069141
Natural varianti320 – 3201G → R in CDLS5. 1 Publication
VAR_069142
Natural varianti334 – 3341H → R in CDLS5. 1 Publication
VAR_069143
Wilson-Turner X-linked mental retardation syndrome (WTS) [MIM:309585]: A neurologic disorder characterized by severe intellectual disability, dysmorphic facial features, hypogonadism, short stature, and truncal obesity. Affected females have a milder phenotype than affected males.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi39 – 391S → A: Enhances the deacetylase activity. 1 Publication
Mutagenesisi39 – 391S → E: Decreases the deacetylase activity. 1 Publication
Mutagenesisi101 – 1011D → A: Complete loss of catalytical activity. Complete loss of catalytical activity; when associated with F-306. 2 Publications
Mutagenesisi101 – 1011D → E: Partial loss of catalytical activity. 2 Publications
Mutagenesisi101 – 1011D → L: Complete loss of catalytical activity. 2 Publications
Mutagenesisi101 – 1011D → N: Almost complete loss of catalytical activity. 2 Publications
Mutagenesisi142 – 1432HH → AA: Strongly reduces histone deacetylase activity. 1 Publication
Mutagenesisi143 – 1431H → A: Loss of catalytic activity. 1 Publication
Mutagenesisi306 – 3061Y → F: Loss of catalytic activity. Complete loss of catalytic activity; when associated with A-101. 1 Publication

Keywords - Diseasei

Disease mutation, Mental retardation, Obesity

Organism-specific databases

MIMi300882. phenotype.
309585. phenotype.
Orphaneti199. Cornelia de Lange syndrome.
3459. Wilson-Turner syndrome.
PharmGKBiPA37766.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 377377Histone deacetylase 8PRO_0000114708Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei39 – 391Phosphoserine1 Publication

Post-translational modificationi

Phosphorylated by PKA on serine 39. Phosphorylation reduces deacetylase activity observed preferentially on histones H3 and H4.2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ9BY41.
PaxDbiQ9BY41.
PRIDEiQ9BY41.

PTM databases

PhosphoSiteiQ9BY41.

Expressioni

Tissue specificityi

Weakly expressed in most tissues. Expressed at higher level in heart, brain, kidney and pancreas and also in liver, lung, placenta, prostate and kidney.4 Publications

Gene expression databases

BgeeiQ9BY41.
CleanExiHS_HDAC8.
ExpressionAtlasiQ9BY41. baseline and differential.
GenevestigatoriQ9BY41.

Organism-specific databases

HPAiHPA048560.

Interactioni

Subunit structurei

Interacts with PEPB2-MYH11, a fusion protein consisting of the 165 N-terminal residues of CBF-beta (PEPB2) with the tail region of MYH11 produced by the inversion Inv(16)(p13q22), a translocation associated with acute myeloid leukemia of M4EO subtype. The PEPB2-MYH1 fusion protein also interacts with RUNX1, a well known transcriptional regulator, suggesting that the interaction with HDAC8 may participate in the conversion of RUNX1 into a constitutive transcriptional repressor. Interacts with CBFA2T3. Interacts with phosphorylated SMG5/EST1B; this interaction protects SMG5 from ubiquitin-mediated degradation. Associates with alpha-SMA (smooth muscle alpha-actin).4 Publications

Protein-protein interaction databases

BioGridi120968. 94 interactions.
IntActiQ9BY41. 16 interactions.
MINTiMINT-5207407.
STRINGi9606.ENSP00000362674.

Structurei

Secondary structure

1
377
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi17 – 193Combined sources
Helixi22 – 287Combined sources
Beta strandi31 – 344Combined sources
Helixi37 – 4711Combined sources
Helixi50 – 534Combined sources
Beta strandi54 – 574Combined sources
Helixi64 – 674Combined sources
Turni68 – 703Combined sources
Helixi73 – 8311Combined sources
Turni84 – 863Combined sources
Turni91 – 977Combined sources
Beta strandi99 – 1024Combined sources
Helixi108 – 12720Combined sources
Beta strandi128 – 1303Combined sources
Beta strandi132 – 1365Combined sources
Beta strandi153 – 1553Combined sources
Helixi157 – 1659Combined sources
Turni166 – 1683Combined sources
Beta strandi170 – 1767Combined sources
Beta strandi178 – 1803Combined sources
Helixi183 – 1886Combined sources
Turni189 – 1913Combined sources
Beta strandi193 – 20210Combined sources
Beta strandi207 – 2093Combined sources
Helixi220 – 2223Combined sources
Beta strandi226 – 2316Combined sources
Helixi237 – 25519Combined sources
Beta strandi258 – 2636Combined sources
Helixi266 – 2683Combined sources
Helixi281 – 29212Combined sources
Beta strandi297 – 3015Combined sources
Helixi308 – 32215Combined sources
Helixi337 – 3404Combined sources
Turni341 – 3433Combined sources
Helixi359 – 37315Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1T64X-ray1.90A/B1-377[»]
1T67X-ray2.31A1-377[»]
1T69X-ray2.91A1-377[»]
1VKGX-ray2.20A/B1-377[»]
1W22X-ray2.50A/B1-377[»]
2V5WX-ray2.00A/B1-377[»]
2V5XX-ray2.25A/B1-377[»]
3EW8X-ray1.80A1-377[»]
3EWFX-ray2.50A/B/C/D1-377[»]
3EZPX-ray2.65A/B1-377[»]
3EZTX-ray2.85A/B1-377[»]
3F06X-ray2.55A/B1-377[»]
3F07X-ray3.30A/B/C1-377[»]
3F0RX-ray2.54A/B/C1-377[»]
3MZ3X-ray3.20A/B1-377[»]
3MZ4X-ray1.84A/B1-377[»]
3MZ6X-ray2.00A1-377[»]
3MZ7X-ray1.90A1-377[»]
3RQDX-ray2.14A/B1-377[»]
3SFFX-ray2.00A1-377[»]
3SFHX-ray2.70A1-377[»]
4QA0X-ray2.24A/B1-377[»]
4QA1X-ray1.92A/B/C/D1-377[»]
4QA2X-ray2.38A/B1-377[»]
4QA3X-ray2.88A/B1-377[»]
4QA4X-ray1.98A1-377[»]
4QA5X-ray1.76A/B1-377[»]
4QA6X-ray2.05A/B1-377[»]
4QA7X-ray2.31A1-377[»]
ProteinModelPortaliQ9BY41.
SMRiQ9BY41. Positions 14-377.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9BY41.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 324311Histone deacetylaseAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0123.
GeneTreeiENSGT00530000062889.
HOGENOMiHOG000225180.
HOVERGENiHBG057112.
InParanoidiQ9BY41.
KOiK11405.
OMAiCLIDGKC.
PhylomeDBiQ9BY41.
TreeFamiTF106175.

Family and domain databases

Gene3Di3.40.800.20. 1 hit.
InterProiIPR000286. His_deacetylse.
IPR003084. His_deacetylse_1.
IPR023801. His_deacetylse_dom.
[Graphical view]
PANTHERiPTHR10625. PTHR10625. 1 hit.
PfamiPF00850. Hist_deacetyl. 1 hit.
[Graphical view]
PIRSFiPIRSF037913. His_deacetylse_1. 1 hit.
PRINTSiPR01270. HDASUPER.
PR01271. HISDACETLASE.

Sequences (8)i

Sequence statusi: Complete.

This entry describes 8 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9BY41-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MEEPEEPADS GQSLVPVYIY SPEYVSMCDS LAKIPKRASM VHSLIEAYAL
60 70 80 90 100
HKQMRIVKPK VASMEEMATF HTDAYLQHLQ KVSQEGDDDH PDSIEYGLGY
110 120 130 140 150
DCPATEGIFD YAAAIGGATI TAAQCLIDGM CKVAINWSGG WHHAKKDEAS
160 170 180 190 200
GFCYLNDAVL GILRLRRKFE RILYVDLDLH HGDGVEDAFS FTSKVMTVSL
210 220 230 240 250
HKFSPGFFPG TGDVSDVGLG KGRYYSVNVP IQDGIQDEKY YQICESVLKE
260 270 280 290 300
VYQAFNPKAV VLQLGADTIA GDPMCSFNMT PVGIGKCLKY ILQWQLATLI
310 320 330 340 350
LGGGGYNLAN TARCWTYLTG VILGKTLSSE IPDHEFFTAY GPDYVLEITP
360 370
SCRPDRNEPH RIQQILNYIK GNLKHVV
Length:377
Mass (Da):41,758
Last modified:April 11, 2003 - v2
Checksum:iCAA1B91894FB5013
GO
Isoform 2 (identifier: Q9BY41-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     248-272: LKEVYQAFNPKAVVLQLGADTIAGD → RTSCPKSRPVEAAAAACLPHLHSLV
     273-377: Missing.

Note: Derived from EST data.

Show »
Length:272
Mass (Da):29,944
Checksum:i060E9B19659F4A91
GO
Isoform 3 (identifier: Q9BY41-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     147-163: DEASGFCYLNDAVLGIL → RDVCVCGTLQGILKKSK
     164-377: Missing.

Show »
Length:163
Mass (Da):17,880
Checksum:i06E2B3E76A5D6B0D
GO
Isoform 4 (identifier: Q9BY41-4) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     56-146: Missing.

Note: No experimental confirmation available.

Show »
Length:286
Mass (Da):31,935
Checksum:iB69361BAC77E90E2
GO
Isoform 5 (identifier: Q9BY41-5) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     246-272: SVLKEVYQAFNPKAVVLQLGADTIAGD → RYEPPAPNPGL
     273-377: Missing.

Note: No experimental confirmation available.

Show »
Length:256
Mass (Da):28,353
Checksum:i175AB23C2589926F
GO
Isoform 6 (identifier: Q9BY41-6) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     56-146: Missing.
     185-210: Missing.
     246-256: SVLKEVYQAFN → RYEPPAPNPGL
     257-377: Missing.

Note: Gene prediction based on EST data.

Show »
Length:139
Mass (Da):15,685
Checksum:iE46FD4F32AAABC43
GO
Isoform 7 (identifier: Q9BY41-7) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     147-158: DEASGFCYLNDA → ETCVYVALYKAF
     159-377: Missing.

Note: Gene prediction based on EST data.

Show »
Length:158
Mass (Da):17,439
Checksum:iF7EFADF18566BB00
GO
Isoform 8 (identifier: Q9BY41-8) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     147-377: Missing.

Note: No experimental confirmation available.

Show »
Length:146
Mass (Da):16,050
Checksum:i5234C861058EAE1B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti31 – 311L → P in AAH50433. (PubMed:15489334)Curated
Sequence conflicti179 – 1791L → V no nucleotide entry (PubMed:10756090)Curated
Sequence conflicti223 – 2231R → W in AAF73428. (PubMed:10926844)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti180 – 1801H → R in CDLS5. 1 Publication
VAR_069140
Natural varianti311 – 3111T → M in CDLS5. 1 Publication
VAR_069141
Natural varianti320 – 3201G → R in CDLS5. 1 Publication
VAR_069142
Natural varianti334 – 3341H → R in CDLS5. 1 Publication
VAR_069143

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei56 – 14691Missing in isoform 4 and isoform 6. 1 PublicationVSP_043426Add
BLAST
Alternative sequencei147 – 377231Missing in isoform 8. 1 PublicationVSP_047502Add
BLAST
Alternative sequencei147 – 16317DEASG…VLGIL → RDVCVCGTLQGILKKSK in isoform 3. 1 PublicationVSP_007174Add
BLAST
Alternative sequencei147 – 15812DEASG…YLNDA → ETCVYVALYKAF in isoform 7. CuratedVSP_046832Add
BLAST
Alternative sequencei159 – 377219Missing in isoform 7. CuratedVSP_046833Add
BLAST
Alternative sequencei164 – 377214Missing in isoform 3. 1 PublicationVSP_007175Add
BLAST
Alternative sequencei185 – 21026Missing in isoform 6. CuratedVSP_046834Add
BLAST
Alternative sequencei246 – 27227SVLKE…TIAGD → RYEPPAPNPGL in isoform 5. 1 PublicationVSP_043427Add
BLAST
Alternative sequencei246 – 25611SVLKEVYQAFN → RYEPPAPNPGL in isoform 6. CuratedVSP_046835Add
BLAST
Alternative sequencei248 – 27225LKEVY…TIAGD → RTSCPKSRPVEAAAAACLPH LHSLV in isoform 2. 1 PublicationVSP_007176Add
BLAST
Alternative sequencei257 – 377121Missing in isoform 6. CuratedVSP_046836Add
BLAST
Alternative sequencei273 – 377105Missing in isoform 2 and isoform 5. 2 PublicationsVSP_007177Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF230097 mRNA. Translation: AAF73076.1.
AF245664 mRNA. Translation: AAF73428.1.
AJ277724 mRNA. Translation: CAB90213.1.
BQ189619 mRNA. No translation available.
AK296641 mRNA. Translation: BAG59242.1.
AK300895 mRNA. Translation: BAG62534.1.
AA376331 mRNA. No translation available.
AI159768 mRNA. No translation available.
T99283 mRNA. No translation available.
AF212246 mRNA. Translation: AAK14930.1.
AL133500 Genomic DNA. No translation available.
BX295542 Genomic DNA. No translation available.
BC050433 mRNA. Translation: AAH50433.1.
CCDSiCCDS14420.1. [Q9BY41-1]
CCDS55448.1. [Q9BY41-6]
CCDS55449.1. [Q9BY41-4]
CCDS55450.1. [Q9BY41-8]
CCDS55451.1. [Q9BY41-5]
CCDS55452.1. [Q9BY41-7]
RefSeqiNP_001159890.1. NM_001166418.1. [Q9BY41-4]
NP_001159891.1. NM_001166419.1. [Q9BY41-5]
NP_001159892.1. NM_001166420.1. [Q9BY41-8]
NP_001159894.1. NM_001166422.1. [Q9BY41-7]
NP_001159920.1. NM_001166448.1. [Q9BY41-6]
NP_060956.1. NM_018486.2. [Q9BY41-1]
UniGeneiHs.310536.

Genome annotation databases

EnsembliENST00000373554; ENSP00000362655; ENSG00000147099. [Q9BY41-8]
ENST00000373556; ENSP00000362657; ENSG00000147099. [Q9BY41-7]
ENST00000373559; ENSP00000362660; ENSG00000147099. [Q9BY41-6]
ENST00000373573; ENSP00000362674; ENSG00000147099. [Q9BY41-1]
ENST00000373589; ENSP00000362691; ENSG00000147099. [Q9BY41-4]
ENST00000439122; ENSP00000414486; ENSG00000147099. [Q9BY41-5]
GeneIDi55869.
KEGGihsa:55869.
UCSCiuc004eau.3. human. [Q9BY41-1]
uc004eav.3. human. [Q9BY41-5]
uc011mqg.2. human. [Q9BY41-4]

Polymorphism databases

DMDMi29839394.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF230097 mRNA. Translation: AAF73076.1 .
AF245664 mRNA. Translation: AAF73428.1 .
AJ277724 mRNA. Translation: CAB90213.1 .
BQ189619 mRNA. No translation available.
AK296641 mRNA. Translation: BAG59242.1 .
AK300895 mRNA. Translation: BAG62534.1 .
AA376331 mRNA. No translation available.
AI159768 mRNA. No translation available.
T99283 mRNA. No translation available.
AF212246 mRNA. Translation: AAK14930.1 .
AL133500 Genomic DNA. No translation available.
BX295542 Genomic DNA. No translation available.
BC050433 mRNA. Translation: AAH50433.1 .
CCDSi CCDS14420.1. [Q9BY41-1 ]
CCDS55448.1. [Q9BY41-6 ]
CCDS55449.1. [Q9BY41-4 ]
CCDS55450.1. [Q9BY41-8 ]
CCDS55451.1. [Q9BY41-5 ]
CCDS55452.1. [Q9BY41-7 ]
RefSeqi NP_001159890.1. NM_001166418.1. [Q9BY41-4 ]
NP_001159891.1. NM_001166419.1. [Q9BY41-5 ]
NP_001159892.1. NM_001166420.1. [Q9BY41-8 ]
NP_001159894.1. NM_001166422.1. [Q9BY41-7 ]
NP_001159920.1. NM_001166448.1. [Q9BY41-6 ]
NP_060956.1. NM_018486.2. [Q9BY41-1 ]
UniGenei Hs.310536.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1T64 X-ray 1.90 A/B 1-377 [» ]
1T67 X-ray 2.31 A 1-377 [» ]
1T69 X-ray 2.91 A 1-377 [» ]
1VKG X-ray 2.20 A/B 1-377 [» ]
1W22 X-ray 2.50 A/B 1-377 [» ]
2V5W X-ray 2.00 A/B 1-377 [» ]
2V5X X-ray 2.25 A/B 1-377 [» ]
3EW8 X-ray 1.80 A 1-377 [» ]
3EWF X-ray 2.50 A/B/C/D 1-377 [» ]
3EZP X-ray 2.65 A/B 1-377 [» ]
3EZT X-ray 2.85 A/B 1-377 [» ]
3F06 X-ray 2.55 A/B 1-377 [» ]
3F07 X-ray 3.30 A/B/C 1-377 [» ]
3F0R X-ray 2.54 A/B/C 1-377 [» ]
3MZ3 X-ray 3.20 A/B 1-377 [» ]
3MZ4 X-ray 1.84 A/B 1-377 [» ]
3MZ6 X-ray 2.00 A 1-377 [» ]
3MZ7 X-ray 1.90 A 1-377 [» ]
3RQD X-ray 2.14 A/B 1-377 [» ]
3SFF X-ray 2.00 A 1-377 [» ]
3SFH X-ray 2.70 A 1-377 [» ]
4QA0 X-ray 2.24 A/B 1-377 [» ]
4QA1 X-ray 1.92 A/B/C/D 1-377 [» ]
4QA2 X-ray 2.38 A/B 1-377 [» ]
4QA3 X-ray 2.88 A/B 1-377 [» ]
4QA4 X-ray 1.98 A 1-377 [» ]
4QA5 X-ray 1.76 A/B 1-377 [» ]
4QA6 X-ray 2.05 A/B 1-377 [» ]
4QA7 X-ray 2.31 A 1-377 [» ]
ProteinModelPortali Q9BY41.
SMRi Q9BY41. Positions 14-377.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 120968. 94 interactions.
IntActi Q9BY41. 16 interactions.
MINTi MINT-5207407.
STRINGi 9606.ENSP00000362674.

Chemistry

BindingDBi Q9BY41.
ChEMBLi CHEMBL3192.
DrugBanki DB02546. Vorinostat.
GuidetoPHARMACOLOGYi 2619.

PTM databases

PhosphoSitei Q9BY41.

Polymorphism databases

DMDMi 29839394.

Proteomic databases

MaxQBi Q9BY41.
PaxDbi Q9BY41.
PRIDEi Q9BY41.

Protocols and materials databases

DNASUi 55869.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000373554 ; ENSP00000362655 ; ENSG00000147099 . [Q9BY41-8 ]
ENST00000373556 ; ENSP00000362657 ; ENSG00000147099 . [Q9BY41-7 ]
ENST00000373559 ; ENSP00000362660 ; ENSG00000147099 . [Q9BY41-6 ]
ENST00000373573 ; ENSP00000362674 ; ENSG00000147099 . [Q9BY41-1 ]
ENST00000373589 ; ENSP00000362691 ; ENSG00000147099 . [Q9BY41-4 ]
ENST00000439122 ; ENSP00000414486 ; ENSG00000147099 . [Q9BY41-5 ]
GeneIDi 55869.
KEGGi hsa:55869.
UCSCi uc004eau.3. human. [Q9BY41-1 ]
uc004eav.3. human. [Q9BY41-5 ]
uc011mqg.2. human. [Q9BY41-4 ]

Organism-specific databases

CTDi 55869.
GeneCardsi GC0XM071549.
GeneReviewsi HDAC8.
HGNCi HGNC:13315. HDAC8.
HPAi HPA048560.
MIMi 300269. gene.
300882. phenotype.
309585. phenotype.
neXtProti NX_Q9BY41.
Orphaneti 199. Cornelia de Lange syndrome.
3459. Wilson-Turner syndrome.
PharmGKBi PA37766.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0123.
GeneTreei ENSGT00530000062889.
HOGENOMi HOG000225180.
HOVERGENi HBG057112.
InParanoidi Q9BY41.
KOi K11405.
OMAi CLIDGKC.
PhylomeDBi Q9BY41.
TreeFami TF106175.

Enzyme and pathway databases

BRENDAi 3.5.1.98. 2681.
Reactomei REACT_118780. NOTCH1 Intracellular Domain Regulates Transcription.
REACT_150425. Resolution of Sister Chromatid Cohesion.
REACT_150471. Separation of Sister Chromatids.
REACT_160243. Constitutive Signaling by NOTCH1 PEST Domain Mutants.
REACT_160254. Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants.
REACT_228222. HDACs deacetylate histones.
SABIO-RK Q9BY41.

Miscellaneous databases

ChiTaRSi HDAC8. human.
EvolutionaryTracei Q9BY41.
GeneWikii HDAC8.
GenomeRNAii 55869.
NextBioi 61182.
PROi Q9BY41.
SOURCEi Search...

Gene expression databases

Bgeei Q9BY41.
CleanExi HS_HDAC8.
ExpressionAtlasi Q9BY41. baseline and differential.
Genevestigatori Q9BY41.

Family and domain databases

Gene3Di 3.40.800.20. 1 hit.
InterProi IPR000286. His_deacetylse.
IPR003084. His_deacetylse_1.
IPR023801. His_deacetylse_dom.
[Graphical view ]
PANTHERi PTHR10625. PTHR10625. 1 hit.
Pfami PF00850. Hist_deacetyl. 1 hit.
[Graphical view ]
PIRSFi PIRSF037913. His_deacetylse_1. 1 hit.
PRINTSi PR01270. HDASUPER.
PR01271. HISDACETLASE.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and characterization of a novel human class I histone deacetylase that functions as a transcription repressor."
    Hu E., Chen Z., Fredrickson T., Zhu Y., Kirkpatrick R., Zhang G.-F., Johanson K., Sung C.-M., Liu R., Winkler J.
    J. Biol. Chem. 275:15254-15264(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), CHARACTERIZATION, FUNCTION.
    Tissue: Kidney.
  2. "Cloning and characterization of a novel human histone deacetylase, HDAC8."
    Buggy J.J., Sideris M.L., Mak P., Lorimer D.D., McIntosh B., Clark J.M.
    Biochem. J. 350:199-205(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, FUNCTION, MUTAGENESIS OF 142-HIS-HIS-143.
    Tissue: Uterus.
  3. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), CHARACTERIZATION, FUNCTION.
    Tissue: Heart.
  4. "Characterization of a highly complex region in Xq13 and mapping of three isodicentric breakpoints associated with preleukemia."
    McDonell N., Ramser J., Francis F., Vinet M.-C., Rider S., Sudbrak R., Riesselman L., Yaspo M.-L., Reinhardt R., Monaco A.P., Ross F., Kahn A., Kearney L., Buckle V., Chelly J.
    Genomics 64:221-229(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
  5. "Normalization and subtraction: two approaches to facilitate gene discovery."
    Bonaldo M.F., Lennon G., Soares M.B.
    Genome Res. 6:791-806(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 8).
  6. "A novel gene expressed in human pheochromocytoma."
    Li Y., Huang Q., Peng Y., Song H., Yu Y., Xu S., Ren S., Chen Z., Han Z.
    Submitted (DEC-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
    Tissue: Pheochromocytoma.
  7. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 4 AND 5).
    Tissue: Colon and Small intestine.
  8. "The DNA sequence of the human X chromosome."
    Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.
    , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
    Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  9. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Lung.
  10. "ETO, a target of t(8;21) in acute leukemia, makes distinct contacts with multiple histone deacetylases and binds mSin3A through its oligomerization domain."
    Amann J.M., Nip J., Strom D.K., Lutterbach B., Harada H., Lenny N., Downing J.R., Meyers S., Hiebert S.W.
    Mol. Cell. Biol. 21:6470-6483(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH CBFA2T3.
  11. "The inv(16) fusion protein associates with corepressors via a smooth muscle myosin heavy-chain domain."
    Durst K.L., Lutterbach B., Kummalue T., Friedman A.D., Hiebert S.W.
    Mol. Cell. Biol. 23:607-619(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH PEPB2-MYH11 FUSION PROTEIN.
  12. "Negative regulation of histone deacetylase 8 activity by cyclic AMP-dependent protein kinase A."
    Lee H., Rezai-Zadeh N., Seto E.
    Mol. Cell. Biol. 24:765-773(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION BY PKA, MUTAGENESIS OF SER-39, FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
  13. "Histone deacetylase HDAC8 associates with smooth muscle alpha-actin and is essential for smooth muscle cell contractility."
    Waltregny D., Glenisson W., Tran S.L., North B.J., Verdin E., Colige A., Castronovo V.
    FASEB J. 19:966-968(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
  14. "Use of histone deacetylase 8 (HDAC8), a new marker of smooth muscle differentiation, in the classification of mesenchymal tumors of the uterus."
    de Leval L., Waltregny D., Boniver J., Young R.H., Castronovo V., Oliva E.
    Am. J. Surg. Pathol. 30:319-327(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
  15. "Histone deacetylase 8 safeguards the human ever-shorter telomeres 1B (hEST1B) protein from ubiquitin-mediated degradation."
    Lee H., Sengupta N., Villagra A., Rezai-Zadeh N., Seto E.
    Mol. Cell. Biol. 26:5259-5269(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SMG5.
  16. "X-exome sequencing identifies a HDAC8 variant in a large pedigree with X-linked intellectual disability, truncal obesity, gynaecomastia, hypogonadism and unusual face."
    Harakalova M., van den Boogaard M.J., Sinke R., van Lieshout S., van Tuil M.C., Duran K., Renkens I., Terhal P.A., de Kovel C., Nijman I.J., van Haelst M., Knoers N.V., van Haaften G., Kloosterman W., Hennekam R.C., Cuppen E., Ploos van Amstel H.K.
    J. Med. Genet. 49:539-543(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: INVOLVEMENT IN WTS.
  17. Cited for: FUNCTION, VARIANTS CDLS5 ARG-180; MET-311; ARG-320 AND ARG-334.
  18. Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEXES WITH TSA; SAHA; MS-344; CRA-A AND DIVALENT METAL CATION, ENZYME REGULATION, PHOSPHORYLATION AT SER-39.
  19. "Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex."
    Vannini A., Volpari C., Gallinari P., Jones P., Mattu M., Carfi A., De Francesco R., Steinkuehler C., Di Marco S.
    EMBO Rep. 8:879-884(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH DIVALENT METAL CATION, MUTAGENESIS OF ASP-101 AND TYR-306.
  20. "Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors."
    Dowling D.P., Gantt S.L., Gattis S.G., Fierke C.A., Christianson D.W.
    Biochemistry 47:13554-13563(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.31 ANGSTROMS) IN COMPLEXES WITH PEPTIDE SUBSTRATE; SAHA; TSA; M-344 AND APHA, ACTIVE SITE, MUTAGENESIS OF ASP-101 AND HIS-143.

Entry informationi

Entry nameiHDAC8_HUMAN
AccessioniPrimary (citable) accession number: Q9BY41
Secondary accession number(s): A6ND12
, A6ND61, A6NET3, A6NJR3, A8MQ62, B4DKN0, B4DV22, Q86VC8, Q9NP76, Q9NYH4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 11, 2003
Last sequence update: April 11, 2003
Last modified: November 26, 2014
This is version 128 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3